tek::Haploid Class Reference

Haploid class. More...

#include <haploid.hpp>

Public Types
using	param_type = HaploidParams
	Alias.
using	URBG = pcglite::pcg64
	random number generator class
using	position_t = int32_t
	unsigned integer type for TE position

Public Member Functions
	Haploid ()=default
	default constructor
	Haploid (size_t, URBG &)
	constructor for recombination test
	Haploid (const Haploid &)=default
	default copy constructor
	Haploid (Haploid &&other)=default
	default move constructor
Haploid &	operator= (Haploid &&)=default
	default move assignment operator
Haploid	gametogenesis (const Haploid &other, URBG &engine) const
	return a Haploid object after recombination
void	transpose_mutate (Haploid &other, URBG &engine)
	mutation process within an individual
bool	hyperactivate ()
	introduce a hyperactivating mutation
double	fitness (const Haploid &) const
	evaluate and return fitness
std::vector< std::string >	summarize () const
	return vector of Transposon summaries
std::ostream &	write_fasta (std::ostream &) const
	write sequence with address as name
bool	empty () const
	shortcut of sites_.empty()
auto	begin () const
	shortcut of sites_.begin()
auto	end () const
	shortcut of sites_.end()

Static Public Member Functions
static Haploid	copy_founder ()
	return a Haploid with an ORIGINAL_TE_ on the same site
static void	initialize (size_t popsize, double theta, double rho)
	set static member variables
static void	insert_coefs_gp (size_t)
	testing function to check distribution of SELECTION_COEFS_GP_
static const std::unordered_map< position_t, double > &	SELECTION_COEFS_GP ()
	getter of SELECTION_COEFS_GP_
static void	param (const param_type &p)
	Set PARAM_.
static const param_type &	param ()
	Get PARAM_.

Private Member Functions
Haploid &	operator= (const Haploid &)=default
	default copy assignment operator (private)
std::vector< std::shared_ptr< Transposon > >	transpose (URBG &)
	return TEs to be transposed
void	mutate (URBG &)
	make point mutation, indel, and speciation
double	prod_1_zs () const
	calculate genome position component of fitness

Static Private Member Functions
static position_t	SELECTION_COEFS_GP_emplace (URBG &)
	insert an element into SELECTION_COEFS_GP_ and return its key
static std::set< position_t >	sample_chiasmata (URBG &)
	sample integers for recombination

Private Attributes
std::map< position_t, std::shared_ptr< Transposon > >	sites_
	position => shptr to transposon

Static Private Attributes
static param_type	PARAM_
	Parameters shared among instances.
static constexpr double	INDEL_RATIO_ = 0.2
	\(\phi\), relative rate of indels to point mutation
static constexpr double	TAU_ = 1.5
	\(\tau\), constant for the intensity of copy number selection
static constexpr double	PROP_FUNCTIONAL_SITES_ = 0.75
	\(p\), proportion of non-neutral sites
static double	MUTATION_RATE_ = 0.0
	\(L\mu = L\theta / 4N\), mutation rate per TE
static double	INDEL_RATE_ = 0.0
	\(L\phi\mu\), absolute indel rate per TE
static double	RECOMBINATION_RATE_ = 0.0
	\(c = \rho / 4N\), recombination rate per genome
static std::unordered_map< position_t, double >	SELECTION_COEFS_GP_
	\(s_{GP}\) : coefficient of GP selection
static std::shared_ptr< Transposon >	ORIGINAL_TE_ = std::make_shared<Transposon>()
	original TE with no mutation and complete activity
static std::shared_timed_mutex	MTX_
	readers-writer lock for SELECTION_COEFS_GP_

Friends
std::ostream &	operator<< (std::ostream &ost, const Haploid &x)
	write Haploid.sites_

Detailed Description

Haploid class.

Member Function Documentation

fitness()

double tek::Haploid::fitness

(

const Haploid &

other

)

const

evaluate and return fitness

\[\begin{split} w_k &= w_{GP,k} w_{CN,k} \\ w_{CN,k} &= \prod _{x \in F} \prod _{y \in F} \left(1 - I(d _{xy}) \xi n _{x,k} ^{\frac \tau 2} n _{y,k} ^{\frac \tau 2} \right) \\ \end{split}\]

prod_1_zs()

double tek::Haploid::prod_1_zs ( ) const

private

calculate genome position component of fitness

\[ w_{k,GP} = \prod _j^T (1 - z_j s_{GP,j}) \]

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The documentation for this class was generated from the following files:

• src/haploid.hpp
• src/haploid.cpp